1
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Fanara S, Schloesser M, Joris M, De Franco S, Vandevenne M, Kerff F, Hanikenne M, Motte P. The Arabidopsis SR45 splicing factor bridges the splicing machinery and the exon-exon junction complex. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:2280-2298. [PMID: 38180875 DOI: 10.1093/jxb/erae002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 01/04/2024] [Indexed: 01/07/2024]
Abstract
The Arabidopsis splicing factor serine/arginine-rich 45 (SR45) contributes to several biological processes. The sr45-1 loss-of-function mutant exhibits delayed root development, late flowering, unusual numbers of floral organs, shorter siliques with decreased seed sets, narrower leaves and petals, and altered metal distribution. SR45 bears a unique RNA recognition motif (RRM) flanked by one serine/arginine-rich (RS) domain on both sides. Here, we studied the function of each SR45 domains by examining their involvement in: (i) the spatial distribution of SR45; (ii) the establishment of a protein-protein interaction network including spliceosomal and exon-exon junction complex (EJC) components; and (iii) the RNA binding specificity. We report that the endogenous SR45 promoter is active during vegetative and reproductive growth, and that the SR45 protein localizes in the nucleus. We demonstrate that the C-terminal arginine/serine-rich domain is a determinant of nuclear localization. We show that the SR45 RRM domain specifically binds purine-rich RNA motifs via three residues (H101, H141, and Y143), and is also involved in protein-protein interactions. We further show that SR45 bridges both mRNA splicing and surveillance machineries as a partner of EJC core components and peripheral factors, which requires phosphoresidues probably phosphorylated by kinases from both the CLK and SRPK families. Our findings provide insights into the contribution of each SR45 domain to both spliceosome and EJC assemblies.
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Affiliation(s)
- Steven Fanara
- InBioS-PhytoSystems, Functional Genomics and Plant Molecular Imaging, University of Liège, 4000, Liège, Belgium
| | - Marie Schloesser
- InBioS-PhytoSystems, Functional Genomics and Plant Molecular Imaging, University of Liège, 4000, Liège, Belgium
| | - Marine Joris
- InBioS-PhytoSystems, Functional Genomics and Plant Molecular Imaging, University of Liège, 4000, Liège, Belgium
| | - Simona De Franco
- InBioS-Center for Protein Engineering, Laboratory of Biological Macromolecules, University of Liège, 4000, Liège, Belgium
| | - Marylène Vandevenne
- InBioS-Center for Protein Engineering, Laboratory of Biological Macromolecules, University of Liège, 4000, Liège, Belgium
| | - Frédéric Kerff
- InBioS-Center for Protein Engineering, Laboratory of Crystallography, University of Liège, 4000, Liège, Belgium
| | - Marc Hanikenne
- InBioS-PhytoSystems, Translational Plant Biology, University of Liège, 4000, Liège, Belgium
| | - Patrick Motte
- InBioS-PhytoSystems, Functional Genomics and Plant Molecular Imaging, University of Liège, 4000, Liège, Belgium
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2
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Krzysiak TC, Choi YJ, Kim YJ, Yang Y, DeHaven C, Thompson L, Ponticelli R, Mermigos MM, Thomas L, Marquez A, Sipula I, Kemper JK, Jurczak M, Thomas G, Gronenborn AM. Inhibitory protein-protein interactions of the SIRT1 deacetylase are choreographed by post-translational modification. Protein Sci 2024; 33:e4938. [PMID: 38533551 DOI: 10.1002/pro.4938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 12/15/2023] [Accepted: 02/07/2024] [Indexed: 03/28/2024]
Abstract
Regulation of SIRT1 activity is vital to energy homeostasis and plays important roles in many diseases. We previously showed that insulin triggers the epigenetic regulator DBC1 to prime SIRT1 for repression by the multifunctional trafficking protein PACS-2. Here, we show that liver DBC1/PACS-2 regulates the diurnal inhibition of SIRT1, which is critically important for insulin-dependent switch in fuel metabolism from fat to glucose oxidation. We present the x-ray structure of the DBC1 S1-like domain that binds SIRT1 and an NMR characterization of how the SIRT1 N-terminal region engages DBC1. This interaction is inhibited by acetylation of K112 of DBC1 and stimulated by the insulin-dependent phosphorylation of human SIRT1 at S162 and S172, catalyzed sequentially by CK2 and GSK3, resulting in the PACS-2-dependent inhibition of nuclear SIRT1 enzymatic activity and translocation of the deacetylase in the cytoplasm. Finally, we discuss how defects in the DBC1/PACS-2-controlled SIRT1 inhibitory pathway are associated with disease, including obesity and non-alcoholic fatty liver disease.
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Affiliation(s)
- Troy C Krzysiak
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - You-Jin Choi
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea
| | - Yong Joon Kim
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Yunhan Yang
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Christopher DeHaven
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Lariah Thompson
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Ryan Ponticelli
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Mara M Mermigos
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Laurel Thomas
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Andrea Marquez
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Ian Sipula
- Department of Medicine, Division of Endocrinology and Metabolism, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Jongsook Kim Kemper
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana, Urbana, Illinois, USA
| | - Michael Jurczak
- Department of Medicine, Division of Endocrinology and Metabolism, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Gary Thomas
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Angela M Gronenborn
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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3
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Hollmann NM, Jagtap PKA, Linse JB, Ullmann P, Payr M, Murciano B, Simon B, Hub JS, Hennig J. Upstream of N-Ras C-terminal cold shock domains mediate poly(A) specificity in a novel RNA recognition mode and bind poly(A) binding protein. Nucleic Acids Res 2023; 51:1895-1913. [PMID: 36688322 PMCID: PMC9976900 DOI: 10.1093/nar/gkac1277] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 12/21/2022] [Accepted: 12/23/2022] [Indexed: 01/24/2023] Open
Abstract
RNA binding proteins (RBPs) often engage multiple RNA binding domains (RBDs) to increase target specificity and affinity. However, the complexity of target recognition of multiple RBDs remains largely unexplored. Here we use Upstream of N-Ras (Unr), a multidomain RBP, to demonstrate how multiple RBDs orchestrate target specificity. A crystal structure of the three C-terminal RNA binding cold-shock domains (CSD) of Unr bound to a poly(A) sequence exemplifies how recognition goes beyond the classical ππ-stacking in CSDs. Further structural studies reveal several interaction surfaces between the N-terminal and C-terminal part of Unr with the poly(A)-binding protein (pAbp). All interactions are validated by mutational analyses and the high-resolution structures presented here will guide further studies to understand how both proteins act together in cellular processes.
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Affiliation(s)
- Nele Merret Hollmann
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany.,Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, 69117 Heidelberg, Germany
| | - Pravin Kumar Ankush Jagtap
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany.,Chair of Biochemistry IV, Biophysical Chemistry, University of Bayreuth, Universitätsstrasse 30, 95447 Bayreuth, Germany
| | - Johanna-Barbara Linse
- Theoretical Physics, Saarland University, 66123 Saarbrücken, Germany.,Center for Biophysics, Saarland University, 66123 Saarbrücken, Germany
| | - Philip Ullmann
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Marco Payr
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany.,Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, 69117 Heidelberg, Germany
| | - Brice Murciano
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Bernd Simon
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Jochen S Hub
- Theoretical Physics, Saarland University, 66123 Saarbrücken, Germany.,Center for Biophysics, Saarland University, 66123 Saarbrücken, Germany
| | - Janosch Hennig
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany.,Chair of Biochemistry IV, Biophysical Chemistry, University of Bayreuth, Universitätsstrasse 30, 95447 Bayreuth, Germany
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4
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Chaudhary A, Chaurasia PK, Kushwaha S, Chauhan P, Chawade A, Mani A. Correlating multi-functional role of cold shock domain proteins with intrinsically disordered regions. Int J Biol Macromol 2022; 220:743-753. [PMID: 35987358 DOI: 10.1016/j.ijbiomac.2022.08.100] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 07/26/2022] [Accepted: 08/14/2022] [Indexed: 11/05/2022]
Abstract
Cold shock proteins (CSPs) are an ancient and conserved family of proteins. They are renowned for their role in response to low-temperature stress in bacteria and nucleic acid binding activities. In prokaryotes, cold and non-cold inducible CSPs are involved in various cellular and metabolic processes such as growth and development, osmotic oxidation, starvation, stress tolerance, and host cell invasion. In prokaryotes, cold shock condition reduces cell transcription and translation efficiency. Eukaryotic cold shock domain (CSD) proteins are evolved form of prokaryotic CSPs where CSD is flanked by N- and C-terminal domains. Eukaryotic CSPs are multi-functional proteins. CSPs also act as nucleic acid chaperons by preventing the formation of secondary structures in mRNA at low temperatures. In human, CSD proteins play a crucial role in the progression of breast cancer, colon cancer, lung cancer, and Alzheimer's disease. A well-defined three-dimensional structure of intrinsically disordered regions of CSPs family members is still undetermined. In this article, intrinsic disorder regions of CSPs have been explored systematically to understand the pleiotropic role of the cold shock family of proteins.
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Affiliation(s)
- Amit Chaudhary
- Department of Metallurgical Engineering & Materials Science, Indian Institute of Technology Bombay
| | - Pankaj Kumar Chaurasia
- PG Department of Chemistry, L.S. College, Babasaheb Bhimrao Ambedkar Bihar University, Muzaffarpur, Bihar 842001, India
| | - Sandeep Kushwaha
- National Institute of Animal Biotechnology, Hyderabad 500032, India.
| | | | - Aakash Chawade
- Department of Plant Breeding, Swedish University of Agricultural Sciences, 230 53 Alnarp, Sweden.
| | - Ashutosh Mani
- Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, Prayagraj 211004, India.
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5
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Reduced miR-371b-5p expression drives tumor progression via CSDE1/RAC1 regulation in triple-negative breast cancer. Oncogene 2022; 41:3151-3161. [PMID: 35490208 PMCID: PMC9135623 DOI: 10.1038/s41388-022-02326-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 04/11/2022] [Accepted: 04/14/2022] [Indexed: 11/25/2022]
Abstract
Triple-negative breast cancer (TNBC) is the most aggressive subtype of breast cancer; however, specific prognostic biomarkers have not yet been developed. In this study, we identified dysregulated microRNAs (miRNAs) in TNBC by profiling miRNA and mRNA expression. In patients with TNBC, miR-371b-5p expression was reduced, and miR-371b-5p overexpression significantly mitigated TNBC cell growth, migration, and invasion. In addition, we found that expression of cold shock domain-containing protein E1 (CSDE1), a direct target gene of miR-371b-5p, was upregulated in TNBC cells, and inhibition of CSDE1 expression alleviated TNBC cell growth by regulating RAC1 transcription. Mechanistically, CSDE1, phosphorylated C-terminal domain (p-CTD) of RNA polymerase II (RNAPII), and CDK7 form a complex, and downregulation of CSDE1 leads to weak interaction between RNAPII p-CTD and CDK7, resulting in a decrease in RNAPII p-CTD expression to reduce RAC1 transcript levels in CSDE1-deficient TNBC cells. Our data demonstrate that miR-371b-5p is a tumor-suppressive miRNA that regulates the CSDE1/Rac1 axis and could be a potential prognostic biomarker for TNBC.
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6
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A new horizon for the old antibacterial drug clofoctol. Drug Discov Today 2021; 26:1302-1310. [PMID: 33581321 DOI: 10.1016/j.drudis.2021.02.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 01/16/2021] [Accepted: 02/02/2021] [Indexed: 02/07/2023]
Abstract
The synthetic antibacterial drug clofoctol (CFT) has long been used to treat respiratory tract infections in Europe. In recent years, the drug was found to target two biologically important proteins, the Cdc7/Dbf4 protein kinase complex and the mRNA-binding protein cold shock domain containing E1 (CSDE1), also known as upstream-of-N-Ras protein (UNR). These interactions are at the origin of the antitumor activity of CFT, recently evidenced in prostate cancer and neuroglioma. Drug-protein binding models provide a structural basis to guide the design of more potent anticancer compounds. A renewed interest in CFT can be anticipated for the treatment of cancers, and possibly Coronavirus 2019 (COVID-19).
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7
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Heinemann U, Roske Y. Cold-Shock Domains-Abundance, Structure, Properties, and Nucleic-Acid Binding. Cancers (Basel) 2021; 13:cancers13020190. [PMID: 33430354 PMCID: PMC7825780 DOI: 10.3390/cancers13020190] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/05/2021] [Accepted: 01/06/2021] [Indexed: 02/06/2023] Open
Abstract
Simple Summary Proteins are composed of compact domains, often of known three-dimensional structure, and natively unstructured polypeptide regions. The abundant cold-shock domain is among the set of canonical nucleic acid-binding domains and conserved from bacteria to man. Proteins containing cold-shock domains serve a large variety of biological functions, which are mostly linked to DNA or RNA binding. These functions include the regulation of transcription, RNA splicing, translation, stability and sequestration. Cold-shock domains have a simple architecture with a conserved surface ideally suited to bind single-stranded nucleic acids. Because the binding is mostly by non-specific molecular interactions which do not involve the sugar-phosphate backbone, cold-shock domains are not strictly sequence-specific and do not discriminate reliably between DNA and RNA. Many, but not all functions of cold shock-domain proteins in health and disease can be understood based of the physical and structural properties of their cold-shock domains. Abstract The cold-shock domain has a deceptively simple architecture but supports a complex biology. It is conserved from bacteria to man and has representatives in all kingdoms of life. Bacterial cold-shock proteins consist of a single cold-shock domain and some, but not all are induced by cold shock. Cold-shock domains in human proteins are often associated with natively unfolded protein segments and more rarely with other folded domains. Cold-shock proteins and domains share a five-stranded all-antiparallel β-barrel structure and a conserved surface that binds single-stranded nucleic acids, predominantly by stacking interactions between nucleobases and aromatic protein sidechains. This conserved binding mode explains the cold-shock domains’ ability to associate with both DNA and RNA strands and their limited sequence selectivity. The promiscuous DNA and RNA binding provides a rationale for the ability of cold-shock domain-containing proteins to function in transcription regulation and DNA-damage repair as well as in regulating splicing, translation, mRNA stability and RNA sequestration.
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8
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Liu J, Yuan C, Guo T, Wang F, Zeng Y, Ding X, Lu Z, Renqing D, Zhang H, Xu X, Yue Y, Sun X, Niu C, Zhuoga D, Yang B. Genetic signatures of high-altitude adaptation and geographic distribution in Tibetan sheep. Sci Rep 2020; 10:18332. [PMID: 33110149 PMCID: PMC7591910 DOI: 10.1038/s41598-020-75428-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 10/08/2020] [Indexed: 12/29/2022] Open
Abstract
Most sheep breeding programs designed for the tropics and sub-tropics have to take into account the impacts of environmental adaptive traits. However, the genetic mechanism regulating the multiple biological processes driving adaptive responses remains unclear. In this study, we applied a selective sweep analysis by combing 1% top values of Fst and ZHp on both altitude and geographic subpopulations (APS) in 636 indigenous Tibetan sheep breeds. Results show that 37 genes were identified within overlapped genomic regions regarding Fst significantly associated with APS. Out of the 37 genes, we found that 8, 3 and 6 genes at chromosomes (chr.) 13, 23 and 27, respectively, were identified in the genomic regions with 1% top values of ZHp. We further analyzed the INDEL variation of 6 genes at chr.27 (X chromosome) in APS together with corresponding orthologs of 6 genes in Capra, Pantholops, and Bos Taurus. We found that an INDEL was located within 5'UTR region of HAG1 gene. This INDEL of HAG1 was strongly associated with the variation of APS, which was further confirmed by qPCR. Sheep breeds carrying "C-INDEL" of HAG1 have significantly greater body weight, shear amount, corpuscular hemoglobin and globulin levels, but lower body height, than those carrying "CA-INDEL" of HAG1. We concluded that "C-INDEL" variation of HAG1 gene confers better hypoxia tolerance in the highlands of Tibetan and explains well geographic distributions in this population. These results contribute to our understanding of adaptive responses to altitude and geographic adaptation in Tibetan sheep populations and will help to guide future conservation programs for Tibetan sheep native to Qinghai-Tibetan Plateau.
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Affiliation(s)
- Jianbin Liu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of the Chinese Academy of Agricultural Sciences, Jiangouyan Street, Lanzhou, China.
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Jiangouyan Street, Lanzhou, China.
| | - Chao Yuan
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of the Chinese Academy of Agricultural Sciences, Jiangouyan Street, Lanzhou, China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Jiangouyan Street, Lanzhou, China
| | - Tingting Guo
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of the Chinese Academy of Agricultural Sciences, Jiangouyan Street, Lanzhou, China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Jiangouyan Street, Lanzhou, China
| | - Fan Wang
- China Agricultural Veterinarian Biology Science and Technology Co. Ltd, Xujiaping, Lanzhou, China
| | - Yufeng Zeng
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of the Chinese Academy of Agricultural Sciences, Jiangouyan Street, Lanzhou, China
| | - Xuezhi Ding
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of the Chinese Academy of Agricultural Sciences, Jiangouyan Street, Lanzhou, China
| | - Zengkui Lu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of the Chinese Academy of Agricultural Sciences, Jiangouyan Street, Lanzhou, China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Jiangouyan Street, Lanzhou, China
| | - Dingkao Renqing
- Animal Husbandry Science and Research Institute of Gannan Tibet Autonomous Prefecture in China, Hezuo, China
| | - Hao Zhang
- Pizhou Agricultural and Rural Bureau of Jiangsu Province, Parkway Street, Pizhou, China
| | - Xilan Xu
- Pizhou Animal Health Supervision Institute of Jiangsu Province, Xizhong Street, Pizhou, China
| | - Yaojing Yue
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of the Chinese Academy of Agricultural Sciences, Jiangouyan Street, Lanzhou, China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Jiangouyan Street, Lanzhou, China
| | - Xiaoping Sun
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of the Chinese Academy of Agricultural Sciences, Jiangouyan Street, Lanzhou, China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Jiangouyan Street, Lanzhou, China
| | - Chune Niu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of the Chinese Academy of Agricultural Sciences, Jiangouyan Street, Lanzhou, China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Jiangouyan Street, Lanzhou, China
| | - Deqing Zhuoga
- Institute of Livestock Research, Tibet Academy of Agriculture and Animal Science, Lhasa, 850000, China.
| | - Bohui Yang
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of the Chinese Academy of Agricultural Sciences, Jiangouyan Street, Lanzhou, China.
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Jiangouyan Street, Lanzhou, China.
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9
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Zhang J, Fan JS, Li S, Yang Y, Sun P, Zhu Q, Wang J, Jiang B, Yang D, Liu M. Structural basis of DNA binding to human YB-1 cold shock domain regulated by phosphorylation. Nucleic Acids Res 2020; 48:9361-9371. [PMID: 32710623 PMCID: PMC7498358 DOI: 10.1093/nar/gkaa619] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 06/27/2020] [Accepted: 07/14/2020] [Indexed: 12/11/2022] Open
Abstract
Human Y-box binding protein 1 (YB-1) is a multifunctional protein and overexpressed in many types of cancer. It specifically recognizes DNA/RNA through a cold shock domain (CSD) and regulates nucleic acid metabolism. The C-terminal extension of CSD and the phosphorylation of S102 are indispensable for YB-1 function. Until now, the roles of the C-terminal extension and phosphorylation in gene transcription and translation are still largely unknown. Here, we solved the structure of human YB-1 CSD with a C-terminal extension sequence (CSDex). The structure reveals that the extension interacts with several residues in the conventional CSD and adopts a rigid structure instead of being disordered. Either deletion of this extension or phosphorylation of S102 destabilizes the protein and results in partial unfolding. Structural characterization of CSDex in complex with a ssDNA heptamer shows that all the seven nucleotides are involved in DNA-protein interactions and the C-terminal extension provides a unique DNA binding site. Our DNA-binding study indicates that CSDex can recognize more DNA sequences than previously thought and the phosphorylation reduces its binding to ssDNA dramatically. Our results suggest that gene transcription and translation can be regulated by changing the affinity of CSDex binding to DNA and RNA through phosphorylation, respectively.
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Affiliation(s)
- Jingfeng Zhang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan National Laboratory for Optoelectronics, Wuhan 430071, China
| | - Jing-Song Fan
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, 117543, Singapore
| | - Shuangli Li
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan National Laboratory for Optoelectronics, Wuhan 430071, China
| | - Yunhuang Yang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan National Laboratory for Optoelectronics, Wuhan 430071, China
| | - Peng Sun
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan National Laboratory for Optoelectronics, Wuhan 430071, China
| | - Qinjun Zhu
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan National Laboratory for Optoelectronics, Wuhan 430071, China
| | - Jiannan Wang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan National Laboratory for Optoelectronics, Wuhan 430071, China
| | - Bin Jiang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan National Laboratory for Optoelectronics, Wuhan 430071, China
| | - Daiwen Yang
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, 117543, Singapore
| | - Maili Liu
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan National Laboratory for Optoelectronics, Wuhan 430071, China
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10
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Alves ITS, Condinho M, Custódio S, Pereira BF, Fernandes R, Gonçalves V, da Costa PJ, Lacerda R, Marques AR, Martins-Dias P, Nogueira GR, Neves AR, Pinho P, Rodrigues R, Rolo E, Silva J, Travessa A, Leite RP, Sousa A, Romão L. Genetics of personalized medicine: cancer and rare diseases. Cell Oncol (Dordr) 2018; 41:335-341. [PMID: 29633150 DOI: 10.1007/s13402-018-0379-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/21/2018] [Indexed: 12/28/2022] Open
Abstract
The 21st annual meeting of the Portuguese Society of Human Genetics (SPGH), organized by Luísa Romão, Ana Sousa and Rosário Pinto Leite, was held in Caparica, Portugal, from the 16th to the 18th of November 2017. Having entered an era in which personalized medicine is emerging as a paradigm for disease diagnosis, treatment and prevention, the program of this meeting intended to include lectures by leading national and international scientists presenting exceptional findings on the genetics of personalized medicine. Various topics were discussed, including cancer genetics, transcriptome dynamics and novel therapeutics for cancers and rare disorders that are designed to specifically target molecular alterations in individual patients. Several panel discussions were held to emphasize (ethical) issues associated with personalized medicine, including genetic cancer counseling.
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Affiliation(s)
- Inês Teles Siefers Alves
- Department of Cell Biology and Biochemistry, Springer Science + Business Media B.V, Van Godewijckstraat 30, 3311, GX, Dordrecht, The Netherlands.
| | - Manuel Condinho
- Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal
- Biosystems & Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Sónia Custódio
- Medical Genetics Service, Pediatric Department, Hospital Santa Maria, Lisbon, Portugal
| | - Bruna F Pereira
- Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal
- Biosystems & Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Rafael Fernandes
- Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal
- Biosystems & Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Vânia Gonçalves
- Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal
- Biosystems & Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Paulo J da Costa
- Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal
- Biosystems & Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Rafaela Lacerda
- Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal
- Biosystems & Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Ana Rita Marques
- Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal
- Biosystems & Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Patrícia Martins-Dias
- Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal
- Biosystems & Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Gonçalo R Nogueira
- Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal
- Biosystems & Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Ana Rita Neves
- Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal
- Biosystems & Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Patrícia Pinho
- Genetics Laboratory, Hospital Center of Trás-os-Montes and Alto Douro, Vila Real, Portugal
| | - Raquel Rodrigues
- Medical Genetics Service, Pediatric Department, Hospital Santa Maria, Lisbon, Portugal
| | - Eva Rolo
- Medical Genetics Service, Pediatric Department, Hospital Santa Maria, Lisbon, Portugal
| | - Joana Silva
- Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal
- Biosystems & Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - André Travessa
- Medical Genetics Service, Pediatric Department, Hospital Santa Maria, Lisbon, Portugal
| | - Rosário Pinto Leite
- Genetics Laboratory, Hospital Center of Trás-os-Montes and Alto Douro, Vila Real, Portugal
| | - Ana Sousa
- Medical Genetics Service, Pediatric Department, Hospital Santa Maria, Lisbon, Portugal
| | - Luísa Romão
- Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal
- Biosystems & Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisbon, Lisbon, Portugal
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11
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Wurth L, Papasaikas P, Olmeda D, Bley N, Calvo GT, Guerrero S, Cerezo-Wallis D, Martinez-Useros J, García-Fernández M, Hüttelmaier S, Soengas MS, Gebauer F. UNR/CSDE1 Drives a Post-transcriptional Program to Promote Melanoma Invasion and Metastasis. Cancer Cell 2016; 30:694-707. [PMID: 27908735 DOI: 10.1016/j.ccell.2016.10.004] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 06/13/2016] [Accepted: 10/03/2016] [Indexed: 12/11/2022]
Abstract
RNA binding proteins (RBPs) modulate cancer progression through poorly understood mechanisms. Here we show that the RBP UNR/CSDE1 is overexpressed in melanoma tumors and promotes invasion and metastasis. iCLIP sequencing, RNA sequencing, and ribosome profiling combined with in silico studies unveiled sets of pro-metastatic factors coordinately regulated by UNR as part of RNA regulons. In addition to RNA steady-state levels, UNR was found to control many of its targets at the level of translation elongation/termination. Key pro-oncogenic targets of UNR included VIM and RAC1, as validated by loss- and gain-of-function studies. Our results identify UNR as an oncogenic modulator of melanoma progression, unravel the underlying molecular mechanisms, and identify potential targets for this therapeutically challenging malignancy.
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Affiliation(s)
- Laurence Wurth
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Panagiotis Papasaikas
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - David Olmeda
- Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Nadine Bley
- Section Molecular Cell Biology, Institute of Molecular Medicine (IMM), Martin-Luther-University (MLU), 06120 Halle, Germany
| | - Guadalupe T Calvo
- Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Santiago Guerrero
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Daniela Cerezo-Wallis
- Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Javier Martinez-Useros
- Translational Oncology Division, Oncohealth Institute - Health Research Institute - University Hospital "Fundacion Jimenez Diaz", 28040 Madrid, Spain
| | - María García-Fernández
- Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Stefan Hüttelmaier
- Section Molecular Cell Biology, Institute of Molecular Medicine (IMM), Martin-Luther-University (MLU), 06120 Halle, Germany
| | - Maria S Soengas
- Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Fátima Gebauer
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain.
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12
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Yadav BS, Singh S, Shaw AK, Mani A. Structure prediction and docking-based molecular insights of human YB-1 and nucleic acid interaction. J Biomol Struct Dyn 2016; 34:2561-2580. [PMID: 26609765 DOI: 10.1080/07391102.2015.1124050] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Y-box-binding protein 1 (YB-1), a cold shock domain protein, is one of the most conserved nucleic acid-binding proteins. The multifunctional human YB-1 is a member of a large family of proteins with an evolutionary ancient cold shock domain. The presence of a cold shock domain is a specific feature of Y-box-binding proteins and allows attributing them to a wider group of proteins containing a cold shock domain. This protein is involved in a number of cellular processes including proliferation, differentiation and stress response. The YB-1 performs its function both in the cytoplasm and in the cell nucleus. In this study, we present the structure of full-length human YB-1 protein along with investigation of their nucleic acid-binding preferential. The study also focuses on biases for particular purine and pyrimidine bases. The overall goal of this study was to model and validate full-length YB-1 protein and to compare its nucleic acid-binding studies with previous reports.
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Affiliation(s)
- Birendra Singh Yadav
- a Department of Biotechnology , Motilal Nehru National Institute of Technology , Allahabad 211004 , India
| | - Swati Singh
- b Center of Bioinformatics , Nehru Science Center, Institute of Interdisciplinary Studies, University of Allahabad , Allahabad 211002 , India
| | - Amit Kumar Shaw
- c Department of Biotechnology , National Institute of Technology , Durgapur 713209 , India
| | - Ashutosh Mani
- a Department of Biotechnology , Motilal Nehru National Institute of Technology , Allahabad 211004 , India
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